You can increase the maximum InnoDB index prefix size in MySQL 5.6 to 3072 bytes by setting innodb_large_prefix to Yes along with other settings that you'll also need in order to enable that one, discussed here:
http://dev.mysql.com/doc/refman/5.6/en/innodb-parameters.html#sysvar_innodb_large_prefix
These changes should allow these indexes to be valid for InnoDB tables.
With a character set of (I assume) utf8, a VARCHAR(1024) would need 1024 x 3 = 3072 bytes for its index.